6JP8: Rabbit Cav1.1-Bay K8644 Complex
Rabbit Cav1.1-Bay K8644 Complex. Determined by electron microscopy at 2.7 Å resolution. Released 12 Jun 2019.
- Method
- Electron microscopy
- Resolution
- 2.7 Å
- Organism
- Oryctolagus cuniculus
- Chains
- 5
- Atoms
- 21,801
- Mol. weight
- 461.01 kDa
- Ligands
- NAG, C8U, ETA, CA
- Released
- 12 Jun 2019
Explore 6JP8 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6JP8 contains 130 α-helices and 90 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 72 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-48 | 3 | |
| α-helix | 52-70 | 19 | |
| α-helix | 81-85 | 5 | |
| α-helix | 90-102 | 13 | |
| α-helix | 111-114 | 4 | |
| α-helix | 121-142 | 22 | |
| α-helix | 165-174 | 10 | |
| α-helix | 180-182 | 3 | |
| α-helix | 183-191 | 9 | |
| α-helix | 197-218 | 22 | |
| β-strand | 225-228 | 4 | 5 |
| β-strand | 234 | 1 | 5 |
| α-helix | 240-242 | 3 | |
| β-strand | 259-262 | 4 | 5 |
| α-helix | 278-289 | 12 | |
| α-helix | 294-305 | 12 | |
| α-helix | 311-318 | 8 | |
| α-helix | 319-324 | 6 | |
| α-helix | 325-344 | 20 | |
| α-helix | 350-371 | 22 | |
| α-helix | 420-429 | 10 | |
| α-helix | 434-436 | 3 | |
| α-helix | 439-450 | 12 | |
| α-helix | 458-485 | 28 | |
| α-helix | 488-493 | 6 | |
| α-helix | 496-514 | 19 | |
| α-helix | 523-526 | 4 | |
| α-helix | 531-541 | 11 | |
| α-helix | 546-553 | 8 | |
| α-helix | 556-581 | 26 | |
| α-helix | 600-612 | 13 | |
| α-helix | 616-625 | 10 | |
| α-helix | 634-637 | 4 | |
| α-helix | 638-662 | 25 | |
| α-helix | 666-673 | 8 | |
| α-helix | 675-678 | 4 | |
| α-helix | 682-685 | 4 | |
| α-helix | 791-794 | 4 | |
| α-helix | 802-817 | 16 | |
| α-helix | 827-831 | 5 | |
| α-helix | 839-851 | 13 | |
| α-helix | 870-882 | 13 | |
| α-helix | 893-896 | 4 | |
| α-helix | 898-906 | 9 | |
| α-helix | 907-910 | 4 | |
| α-helix | 912-950 | 39 | |
| β-strand | 955-957 | 3 | 6 |
| β-strand | 971-975 | 5 | 7 |
| α-helix | 976-978 | 3 | |
| β-strand | 983-987 | 5 | 7 |
| β-strand | 990-992 | 3 | 6 |
| α-helix | 1000-1011 | 12 | |
| α-helix | 1016-1024 | 9 | |
| α-helix | 1039-1041 | 3 | |
| α-helix | 1042-1048 | 7 | |
| α-helix | 1049-1056 | 8 | |
| α-helix | 1057-1069 | 13 | |
| α-helix | 1070-1072 | 3 | |
| α-helix | 1083-1094 | 12 | |
| α-helix | 1106-1115 | 10 | |
| α-helix | 1118-1136 | 19 | |
| α-helix | 1144-1147 | 4 | |
| α-helix | 1149-1171 | 23 | |
| α-helix | 1175-1178 | 4 | |
| α-helix | 1181-1205 | 25 | |
| α-helix | 1237-1241 | 5 | |
| α-helix | 1242-1248 | 7 | |
| α-helix | 1251-1266 | 16 | |
| α-helix | 1268-1289 | 22 | |
| β-strand | 1292 | 1 | 8 |
| β-strand | 1296 | 1 | 9 |
| β-strand | 1298 | 1 | 9 |
| β-strand | 1301 | 1 | 10 |
| β-strand | 1304 | 1 | 10 |
| α-helix | 1309-1321 | 13 | |
| α-helix | 1325-1330 | 6 | |
| β-strand | 1336 | 1 | 11 |
| α-helix | 1337 | 1 | |
| β-strand | 1338 | 1 | 8 |
| α-helix | 1339 | 1 | |
| β-strand | 1352 | 1 | 11 |
| α-helix | 1357-1382 | 26 | |
| α-helix | 1384-1387 | 4 | |
| α-helix | 1396-1407 | 12 | |
| β-strand | 1416-1417 | 2 | 12 |
| α-helix | 1419-1421 | 3 | |
| α-helix | 1447-1450 | 4 | |
| β-strand | 1461-1462 | 2 | 12 |
| α-helix | 1463-1471 | 9 | |
Chain B: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 79-94 | 16 | |
| α-helix | 100-101 | 2 | |
| β-strand | 103-107 | 5 | 2 |
| β-strand | 111 | 1 | 3 |
| β-strand | 125 | 1 | 2 |
| β-strand | 128 | 1 | 3 |
| β-strand | 133-139 | 7 | 2 |
| β-strand | 144-149 | 6 | 2 |
| β-strand | 156-160 | 5 | 2 |
| α-helix | 161 | 1 | |
| α-helix | 162-170 | 9 | |
Chain C: 9 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 268-271 | 4 | 2 |
| α-helix | 275 | 1 | |
| β-strand | 276-280 | 5 | 4 |
| α-helix | 288-303 | 16 | |
| β-strand | 309-313 | 5 | 4 |
| α-helix | 344-356 | 13 | |
| β-strand | 363-367 | 5 | 4 |
| α-helix | 375-377 | 3 | |
| β-strand | 385-389 | 5 | 4 |
| α-helix | 394-401 | 8 | |
| α-helix | 408-410 | 3 | |
| α-helix | 412-424 | 13 | |
| α-helix | 427-429 | 3 | |
| β-strand | 432-434 | 3 | 4 |
| α-helix | 439-457 | 19 | |
Chain E: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-26 | 19 | |
| β-strand | 48-50 | 3 | 1 |
| β-strand | 56-59 | 4 | 1 |
| β-strand | 79-81 | 3 | 1 |
| α-helix | 105-127 | 23 | |
| α-helix | 137-164 | 28 | |
| α-helix | 182-201 | 20 | |
Chain F: 41 helices, 57 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-37 | 8 | |
| α-helix | 42-52 | 11 | |
| α-helix | 54-64 | 11 | |
| β-strand | 68-72 | 5 | 13 |
| α-helix | 77-108 | 32 | |
| β-strand | 124-125 | 2 | 14 |
| β-strand | 127-128 | 2 | 15 |
| β-strand | 144-145 | 2 | 14 |
| β-strand | 152 | 1 | 16 |
| β-strand | 161 | 1 | 16 |
| β-strand | 162 | 1 | 17 |
| β-strand | 167-169 | 3 | 15 |
| β-strand | 176 | 1 | 18 |
| β-strand | 178 | 1 | 18 |
| α-helix | 179-187 | 9 | |
| α-helix | 188-191 | 4 | |
| α-helix | 192-201 | 10 | |
| β-strand | 208-212 | 5 | 15 |
| β-strand | 217-220 | 4 | 15 |
| β-strand | 222 | 1 | 17 |
| α-helix | 244-250 | 7 | |
| β-strand | 254-261 | 8 | 19 |
| α-helix | 264-266 | 3 | |
| α-helix | 269-283 | 15 | |
| β-strand | 290-296 | 7 | 19 |
| β-strand | 300-302 | 3 | 19 |
| β-strand | 310 | 1 | 19 |
| α-helix | 314-323 | 10 | |
| α-helix | 335-346 | 12 | |
| β-strand | 357-364 | 8 | 19 |
| α-helix | 372-378 | 7 | |
| β-strand | 385-391 | 7 | 19 |
| α-helix | 399-407 | 9 | |
| β-strand | 411-415 | 5 | 19 |
| α-helix | 418-420 | 3 | |
| α-helix | 429-432 | 4 | |
| α-helix | 434-437 | 4 | |
| α-helix | 440-443 | 4 | |
| β-strand | 447-448 | 2 | 15 |
| α-helix | 449-451 | 3 | |
| β-strand | 452-453 | 2 | 15 |
| β-strand | 460-469 | 10 | 15 |
| β-strand | 486-495 | 10 | 15 |
| α-helix | 496-499 | 4 | |
| β-strand | 513-517 | 5 | 20 |
| β-strand | 522 | 1 | 21 |
| β-strand | 523-525 | 3 | 20 |
| α-helix | 533-534 | 2 | |
| α-helix | 543-545 | 3 | |
| β-strand | 562 | 1 | 21 |
| α-helix | 563-566 | 4 | |
| α-helix | 574-579 | 6 | |
| β-strand | 586-595 | 10 | 20 |
| α-helix | 596 | 1 | |
| β-strand | 602-613 | 12 | 20 |
| β-strand | 621-627 | 7 | 20 |
| β-strand | 632-636 | 5 | 13 |
| α-helix | 641-646 | 6 | |
| α-helix | 653-655 | 3 | |
| β-strand | 661-662 | 2 | 22 |
| β-strand | 670 | 1 | 23 |
| α-helix | 679-692 | 14 | |
| β-strand | 700 | 1 | 23 |
| α-helix | 702-712 | 11 | |
| α-helix | 714-718 | 5 | |
| α-helix | 719-723 | 5 | |
| β-strand | 732-734 | 3 | 24 |
| β-strand | 737-739 | 3 | 24 |
| β-strand | 745-746 | 2 | 22 |
| α-helix | 751-753 | 3 | |
| α-helix | 765-772 | 8 | |
| β-strand | 776 | 1 | 25 |
| β-strand | 777-779 | 3 | 24 |
| α-helix | 780-782 | 3 | |
| β-strand | 796-800 | 5 | 24 |
| β-strand | 803-804 | 2 | 26 |
| β-strand | 809-810 | 2 | 26 |
| β-strand | 813-819 | 7 | 24 |
| α-helix | 820 | 1 | |
| α-helix | 821-829 | 9 | |
| β-strand | 851-856 | 6 | 27 |
| β-strand | 861 | 1 | 28 |
| β-strand | 862-865 | 4 | 27 |
| β-strand | 877 | 1 | 28 |
| α-helix | 878-880 | 3 | |
| α-helix | 883-891 | 9 | |
| β-strand | 896-907 | 12 | 29 |
| β-strand | 975-985 | 11 | 29 |
| β-strand | 992-994 | 3 | 27 |
| β-strand | 997-998 | 2 | 30 |
| β-strand | 1003-1004 | 2 | 30 |
| β-strand | 1007-1010 | 4 | 27 |
| β-strand | 1014 | 1 | 25 |
| β-strand | 1017-1022 | 6 | 27 |
| α-helix | 1024-1026 | 3 | |
| β-strand | 1039-1040 | 2 | 29 |
| α-helix | 1046-1049 | 4 | |
| α-helix | 1053-1055 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Voltage-dependent calcium channel gamma-1 subunit | E | protein | 222 | Oryctolagus cuniculus | P19518 (AlphaFold model) |
| Voltage-dependent L-type calcium channel subunit beta-1 | B, C | protein | 450 | Oryctolagus cuniculus | P19517 (AlphaFold model) |
| Voltage-dependent L-type calcium channel subunit alpha-1S | A | protein | 1873 | Oryctolagus cuniculus | P07293 (AlphaFold model) |
| Voltage-dependent calcium channel subunit alpha-2/delta-1 | F | protein | 1046 | Oryctolagus cuniculus | P13806 (AlphaFold model) |
Sequence of entity 1 (E), FASTA
>6JP8_1 Voltage-dependent calcium channel gamma-1 subunit (chains E)
MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR
IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM
GTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSW
SFACACAAFVLLFLGGISLLLFSLPRMPQNPWESCMDAEPEH
Sequence of entity 2 (B, C), FASTA
>6JP8_2 Voltage-dependent L-type calcium channel subunit beta-1 (chains B, C)
QGPHMALRKEAERQALAQLEKAKTKPVAFAVRTNVGYNPSPGDEVPVEGVAITFEPKDFL
HIKEKYNNDWWIGRLVKEGCEVGFIPSPVKLDSLRLLQEQKLRQSRLSSSKSGDNSSSSL
GDVVTGTRRPTPPASGNEMTNLAFELEPLDLEEDEAELGEQSGSAKTSVSSVTTPPPHGT
RIPFFKKTEHVPPYDVVPSMRPIILVGPSLKGYEVTDMMQKALFDFLKHLFDGRISITRV
TADISLAKRSVLNNPSKHIIIERSNTRSSLAEVQSEIERIFELARTLQLVALDADTINHP
AQLSKTSLAPIIVYIKITSPKVLQRLIKSRGKSQSKHLNVQIAASEKLAQCPPEMFDIIL
DENQLEDACEHLAEYLEAYWKATHPPSSTPPNPLLNRTMATAALAASPAPVSNLQVQVLT
SLRRNLSFWGGLETSQRGGGAVPQQQEHAM
Sequence of entity 3 (A), FASTA
>6JP8_3 Voltage-dependent L-type calcium channel subunit alpha-1S (chains A)
MEPSSPQDEGLRKKQPKKPLPEVLPRPPRALFCLTLQNPLRKACISIVEWKPFETIILLT
IFANCVALAVYLPMPEDDNNSLNLGLEKLEYFFLTVFSIEAAMKIIAYGFLFHQDAYLRS
GWNVLDFIIVFLGVFTAILEQVNVIQSNTAPMSSKGAGLDVKALRAFRVLRPLRLVSGVP
SLQVVLNSIFKAMLPLFHIALLVLFMVIIYAIIGLELFKGKMHKTCYYIGTDIVATVENE
KPSPCARTGSGRPCTINGSECRGGWPGPNHGITHFDNFGFSMLTVYQCITMEGWTDVLYW
VNDAIGNEWPWIYFVTLILLGSFFILNLVLGVLSGEFTKEREKAKSRGTFQKLREKQQLE
EDLRGYMSWITQGEVMDVEDLREGKLSLEEGGSDTESLYEIEGLNKIIQFIRHWRQWNRV
FRWKCHDLVKSRVFYWLVILIVALNTLSIASEHHNQPLWLTHLQDIANRVLLSLFTIEML
LKMYGLGLRQYFMSIFNRFDCFVVCSGILELLLVESGAMTPLGISVLRCIRLLRLFKITK
YWTSLSNLVASLLNSIRSIASLLLLLFLFIIIFALLGMQLFGGRYDFEDTEVRRSNFDNF
PQALISVFQVLTGEDWNSVMYNGIMAYGGPSYPGVLVCIYFIILFVCGNYILLNVFLAIA
VDNLAEAESLTSAQKAKAEERKRRKMSRGLPDKTEEEKSVMAKKLEQKPKGEGIPTTAKL
KVDEFESNVNEVKDPYPSADFPGDDEEDEPEIPVSPRPRPLAELQLKEKAVPIPEASSFF
IFSPTNKVRVLCHRIVNATWFTNFILLFILLSSAALAAEDPIRAESVRNQILGYFDIAFT
SVFTVEIVLKMTTYGAFLHKGSFCRNYFNILDLLVVAVSLISMGLESSTISVVKILRVLR
VLRPLRAINRAKGLKHVVQCVFVAIRTIGNIVLVTTLLQFMFACIGVQLFKGKFFSCNDL
SKMTEEECRGYYYVYKDGDPTQMELRPRQWIHNDFHFDNVLSAMMSLFTVSTFEGWPQLL
YRAIDSNEEDMGPVYNNRVEMAIFFIIYIILIAFFMMNIFVGFVIVTFQEQGETEYKNCE
LDKNQRQCVQYALKARPLRCYIPKNPYQYQVWYVVTSSYFEYLMFALIMLNTICLGMQHY
HQSEEMNHISDILNVAFTIIFTLEMILKLLAFKARGYFGDPWNVFDFLIVIGSIIDVILS
EIDTFLASSGGLYCLGGGCGNVDPDESARISSAFFRLFRVMRLIKLLSRAEGVRTLLWTF
IKSFQALPYVALLIVMLFFIYAVIGMQMFGKIALVDGTQINRNNNFQTFPQAVLLLFRCA
TGEAWQEILLACSYGKLCDPESDYAPGEEYTCGTNFAYYYFISFYMLCAFLIINLFVAVI
MDNFDYLTRDWSILGPHHLDEFKAIWAEYDPEAKGRIKHLDVVTLLRRIQPPLGFGKFCP
HRVACKRLVGMNMPLNSDGTVTFNATLFALVRTALKIKTEGNFEQANEELRAIIKKIWKR
TSMKLLDQVIPPIGDDEVTVGKFYATFLIQEHFRKFMKRQEEYYGYRPKKDTVQIQAGLR
TIEEEAAPEIRRTISGDLTAEEELERAMVEAAMEERIFRRTGGLFGQVDTFLERTNSLPP
VMANQRPLQFAEIEMEELESPVFLEDFPQDARTNPLARANTNNANANVAYGNSNHSNNQM
FSSVHCEREFPGEAETPAAGRGALSHSHRALGPHSKPCAGKLNGQLVQPGMPINQAPPAP
CQQPSTDPPERGQRRTSLTGSLQDEAPQRRSSEGSTPRRPAPATALLIQEALVRGGLDTL
AADAGFVTATSQALADACQMEPEEVEVAATELLKARESVQGMASVPGSLSRRSSLGSLDQ
VQGSQETLIPPRP
Sequence of entity 4 (F), FASTA
>6JP8_4 Voltage-dependent calcium channel subunit alpha-2/delta-1 (chains F)
FPSAVTIKSWVDKMQEDLVTLAKTASGVHQLVDIYEKYQDLYTVEPNNARQLVEIAARDI
EKLLSNRSKALVRLALEAEKVQAAHQWREDFASNEVVYYNAKDDLDPEKNDSEPGSQRIK
PVFIDDANFRRQVSYQHAAVHIPTDIYEGSTIVLNELNWTSALDDVFKKNREEDPSLLWQ
VFGSATGLARYYPASPWVDNSRTPNKIDLYDVRRRPWYIQGAASPKDMLILVDVSGSVSG
LTLKLIRTSVSEMLETLSDDDFVNVASFNSNAQDVSCFQHLVQANVRNKKVLKDAVNNIT
AKGITDYKKGFSFAFEQLLNYNVSRANCNKIIMLFTDGGEERAQEIFAKYNKDKKVRVFT
FSVGQHNYDRGPIQWMACENKGYYYEIPSIGAIRINTQEYLDVLGRPMVLAGDKAKQVQW
TNVYLDALELGLVITGTLPVFNITGQFENKTNLKNQLILGVMGVDVSLEDIKRLTPRFTL
CPNGYYFAIDPNGYVLLHPNLQPKPIGVGIPTINLRKRRPNVQNPKSQEPVTLDFLDAEL
ENDIKVEIRNKMIDGESGEKTFRTLVKSQDERYIDKGNRTYTWTPVNGTDYSLALVLPTY
SFYYIKAKIEETITQARYSETLKPDNFEESGYTFLAPRDYCSDLKPSDNNTEFLLNFNEF
IDRKTPNNPSCNTDLINRVLLDAGFTNELVQNYWSKQKNIKGVKARFVVTDGGITRVYPK
EAGENWQENPETYEDSFYKRSLDNDNYVFTAPYFNKSGPGAYESGIMVSKAVEIYIQGKL
LKPAVVGIKIDVNSWIENFTKTSIRDPCAGPVCDCKRNSDVMDCVILDDGGFLLMANHDD
YTNQIGRFFGEIDPSLMRHLVNISVYAFNKSYDYQSVCEPGAAPKQGAGHRSAYVPSIAD
ILQIGWWATAAAWSILQQFLLSLTFPRLLEAADMEDDDFTASMSKQSCITEQTQYFFDND
SKSFSGVLDCGNCSRIFHVEKLMNTNLIFIMVESKGTCPCDTRLLIQAEQTSDGPDPCDM
VKQPRYRKGPDVCFDNNVLEDYTDCG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 8 |
| C8U | methyl (4~{S})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropy… | C16 H15 F3 N2 O4 | 1 |
| ETA | Ethanolamine | C2 H7 N O | 1 |
| CA | Calcium ion | Ca | 2 |
Primary citation
Molecular Basis for Ligand Modulation of a Mammalian Voltage-Gated Ca2+Channel. Zhao, Y., Huang, G., Wu, J. et al. Cell (2019) 177:1495-1506.e12. DOI 10.1016/j.cell.2019.04.043 · PubMed
Other PDB entries of the same protein (UniProt P19518 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6JPA 2.6 Å, Rabbit Cav1.1-Verapamil Complex
- 8E56 2.8 Å, Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone at 2.8…
- 8E57 2.8 Å, Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone and 100…
- 6JP5 2.9 Å, Rabbit Cav1.1-Nifedipine Complex
- 6JPB 2.9 Å, Rabbit Cav1.1-Diltiazem Complex
- 7JPX 2.9 Å, Rabbit Cav1.1 in the presence of 100 micromolar amlodipine in nanodiscs at 2.9 Angstrom…
- 7JPK 3.0 Å, Rabbit Cav1.1 in the presence of 100 micromolar (S)-(-)-Bay K8644 in nanodiscs at 3.0…
- 8E58 3.0 Å, Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone and 1…
- 7JPW 3.2 Å, Rabbit Cav1.1 in the presence of 100 micromolar (R)-(+)-Bay K8644 in nanodiscs at 3.2…
- 7JPL 3.4 Å, Rabbit Cav1.1 in the presence of 10 micromolar (S)-(-)-Bay K8644 in nanodiscs at 3.4…
- 7JPV 3.4 Å, Rabbit Cav1.1 in the presence of 1 micromolar (S)-(-)-Bay K8644 in nanodiscs at 3.4…
- 5GJV 3.6 Å, Structure of the mammalian voltage-gated calcium channel Cav1.1 complex at near atomic…
Browse structure collections
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